8JQ5

Crystal structure of Lactobacillus rhamnosus L-rhamnose isomerase in complex with D-allulose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DE5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293PEG550MME, MES
Crystal Properties
Matthews coefficientSolvent content
2.3146.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.887α = 90
b = 139.445β = 90
c = 146.834γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 2M2020-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7348.941000.1180.1230.0330.99917.513.4192191
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.731.761001.4141.4690.3960.72213.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.7346.23182641944299.990.141740.139360.18671RANDOM21.6
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.08-0.320.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.131
r_dihedral_angle_4_deg18.686
r_dihedral_angle_3_deg14.429
r_dihedral_angle_1_deg6.27
r_rigid_bond_restr4.796
r_long_range_B_refined3.16
r_long_range_B_other3.109
r_scangle_other2.714
r_mcangle_other2.303
r_mcangle_it2.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.131
r_dihedral_angle_4_deg18.686
r_dihedral_angle_3_deg14.429
r_dihedral_angle_1_deg6.27
r_rigid_bond_restr4.796
r_long_range_B_refined3.16
r_long_range_B_other3.109
r_scangle_other2.714
r_mcangle_other2.303
r_mcangle_it2.301
r_scbond_it2.104
r_scbond_other2.104
r_mcbond_it1.737
r_mcbond_other1.716
r_angle_other_deg1.307
r_angle_refined_deg1.262
r_chiral_restr0.06
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13531
Nucleic Acid Atoms
Solvent Atoms827
Heterogen Atoms104

Software

Software
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
REFMACrefinement
MOLREPphasing